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Using CellProfiler to Analyze and Quantify Vascular Morphology.

Liam Campbell¹, Manoj Kumar¹, Simon Turner²

¹University of Manchester, Oxford Road, Manchester, UK.

Methods in Molecular Biology (Clifton, N.J.)

|January 5, 2017

Summary

This summary is machine-generated.

Automate plant xylem image analysis with CellProfiler, a free software. This study details adapting the tool for efficient, large-scale data collection on cell traits like size and number.

Keywords:

Bioinformatics Cell wall CellProfiler Image analysis Lumen Xylem morphology

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Area of Science:

Plant Biology
Bioinformatics
Image Analysis

Background:

Manual data collection in plant science is time-consuming and prone to errors.
Automated image analysis tools can significantly improve efficiency and data accuracy.

Purpose of the Study:

To demonstrate the adaptation of CellProfiler for analyzing xylem tissue cross sections.
To guide researchers in using CellProfiler for automated collection of phenotypic data.

Main Methods:

Utilized CellProfiler, a free and open-source software for automated image analysis.
Developed a step-by-step pipeline for analyzing xylem tissue images.
Configured modules, options, and parameters within CellProfiler for trait quantification.

Main Results:

Successfully adapted CellProfiler to analyze xylem cross sections.
Enabled the collection of quantitative data on cell size, shape, and number.
Provided a reproducible method for high-throughput phenotypic analysis.

Conclusions:

CellProfiler offers a powerful and accessible solution for automating xylem image analysis.
The described pipeline facilitates efficient and accurate data acquisition for plant research.
Researchers can leverage this method to gather extensive phenotypic data for trait analysis.